Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Yap1

Cell type

Cell type Class
Liver
Cell type
Liver
MeSH Description
A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.

Attributes by original data submitter

Sample

source_name
Liver_ChIPSeq_Yap_LSL_7d
strain background
C57BL/6
genotype
ROSA26-rtTA-IRES-EGFP; tetYAP
tissue
liver
treatment
doxycycline food for 7 days
chip antibody
YAP1 63.7 (Santa Cruz, sc-101199)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP experiments, whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 250 bp were immunoprecipitated using different antibodies. For TEAD, dissected liver/tumors were fixed with 1% formaldehyde. For YAP ChIP, fixation was performed by a double step approach with 0.5 M DSG (Di-(N-succinimidyl)-glutarate) and 1% formaldehyde (FA). For ChIP seq, libraries were prepared for Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
26997287
Reads aligned (%)
86.0
Duplicates removed (%)
20.3
Number of peaks
386 (qval < 1E-05)

mm9

Number of total reads
26997287
Reads aligned (%)
85.7
Duplicates removed (%)
20.3
Number of peaks
435 (qval < 1E-05)

Base call quality data from DBCLS SRA